from __future__ import absolute_import, print_function, division from base.trait import GeneralTrait from base import data_set from base.species import TheSpecies from wqflask import user_manager def get_species_dataset_trait(self, start_vars): #assert type(read_genotype) == type(bool()), "Expecting boolean value for read_genotype" self.dataset = data_set.create_dataset(start_vars['dataset']) print("After creating dataset") self.species = TheSpecies(dataset=self.dataset) print("After creating species") self.this_trait = GeneralTrait(dataset=self.dataset, name=start_vars['trait_id'], cellid=None, get_qtl_info=True) print("After creating trait") #if read_genotype: #self.dataset.group.read_genotype_file() #self.genotype = self.dataset.group.genotype def get_trait_db_obs(self, trait_db_list): if isinstance(trait_db_list, basestring): trait_db_list = trait_db_list.split(",") self.trait_list = [] for trait in trait_db_list: data, _separator, hmac = trait.rpartition(':') data = data.strip() assert hmac==user_manager.actual_hmac_creation(data), "Data tampering?" trait_name, dataset_name = data.split(":") dataset_ob = data_set.create_dataset(dataset_name) trait_ob = GeneralTrait(dataset=dataset_ob, name=trait_name, cellid=None) self.trait_list.append((trait_ob, dataset_ob))